Basically, Autotools is really stable software that has a ton of bugfixes in it. You can't just throw that knowledge away. The overhead of unnecessary tests is negligible compared to compilation costs for anything but the most trivial project. And, I'm pretty sure if you ask the mailing list, there's a way to turn off unnecessary checks for a Fortran compiler, probably by specifying the languages to support with AC_LANG or something.
Yeah, it's clunky and obtuse, but it works to give you portability to just about every system, POSIX or not. And the free support is first class if you ever have a problem.
https://queue.acm.org/detail.cfm?id=2349257
A few highlights:
" yet the 31,085 lines of configure for libtool still check if <sys/stat.h> and <stdlib.h> exist, even though the Unixen, which lacked them, had neither sufficient memory to execute libtool nor disks big enough for its 16-MB source code."
"This is probably also why libtool's configure probes no fewer than 26 different names for the Fortran compiler my system does not have, and then spends another 26 tests to find out if each of these nonexistent Fortran compilers supports the -g option."
"so the input files for autoconf happen by copy and paste, often hiding behind increasingly bloated standard macros covering "standard tests" such as those mentioned earlier, which look for compatibility problems not seen in the past 20 years."
Looks pretty horrible to me. I think removing all that might piss off someone but they're refusal to upgrade shouldn't hold back everyone. Besides, why would I want all those tests running if most of them make no sense and it just adds overhead? And in an otherwise-unused language (M4)?
Looks like crap to me. They should get rid of it.